getPercentageOfIdentity

Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.

Parameters:

countGaps - If true, gap positions are counted as mismatches, i.e., the percentage is normalized by the alignment length.
If false, gap positions are not counted, i.e. the percentage is normalized by the number of aligned residue pairs.
See May (2004). "Percent sequence identity: the need to be explicit."